From f0deb3df3bf15d764fc99550bfb4e5764d804103 Mon Sep 17 00:00:00 2001
From: mjbonifa <m.j.boniface@soton.ac.uk>
Date: Wed, 15 Jan 2025 09:39:53 +0000
Subject: [PATCH] Update README.md

---
 README.md | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index fce8669..d30841c 100644
--- a/README.md
+++ b/README.md
@@ -13,17 +13,20 @@
 <br>
 <sup>*</sup>Correspondence to: Jakub J. Dylag, Digital Health and Biomedical Engineering, School of Electronics and Computer Science, Faculty of Engineering and Physical Sciences, University of Southampton, J.J.Dylag@soton.ac.uk
 
-### 🖋 How to cite this work
+### How to cite this work
+
 > Dylag JJ, Chiovoloni R, Akbari A, Fraser SD, Boniface MJ. A Tool for Automating the Curation of Medical Concepts derived from Coding Lists. GitLab [Internet]. May 2024. Available from: https://git.soton.ac.uk/meldb/concepts-processing
 
-## 🙌 Introduction 
+## Introduction 
+
 This project generate the medical coding lists that defines cohort phenotypes used for inclusion criteria in MELD-B. The goal is to automatically prepare a code list from an approved clinical specification of inclusion criteria. 
 
 The output code list is then used by data providers to select MELD-B cohorts. 
 
-## 📃 Method
+## Method
 
 ### Process
+
 1. Approved MELB-B concepts are defined in a CSV spreadsheet (currently PHEN_summary_working.csv).
 2. Imported Code Lists in `/src` are verified against all NHS TRUD registered codes
 3. Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are defined in JSON format within `PHEN_assign_v3.json`. 
@@ -34,6 +37,7 @@ The output code list is then used by data providers to select MELD-B cohorts.
 6. Output Concept Code Lists can be exported into SAIL or any other Data Bank 
 
 ### Medical Coding Standards Supported
+
 | Code Type     | Verification | Maps to                           |
 |---------------|--------------|-----------------------------------|
 | Readv2        | NHS TRUD     | Readv3, SNOMED, ICD10, OPCS4, ATC |
@@ -55,11 +59,12 @@ MELD-B refers to various diagnostic code formats included in target datasets.
 * ICD-10 are codes used in hospital settings and are importnat for the HES linked datasets. 
 * ATC codes are interntionally accepted for the classification of medicinces and maintained by the WHO.
 
-## ⚙️ Setup
+## Setup
 
 - Delete corrupted files that cannot be read with `bash import.sh`
 
 ### Code Translation Tables
+
 1. Due to the licencing of NHS TRUD coding tables, the following resources <mark>must be downloaded separately</mark>:
 	- [nhs_readbrowser_25.0.0_20180401000001](https://isd.digital.nhs.uk/trud/users/guest/filters/2/categories/9/items/8/releases)
 	- [nhs_datamigration_29.0.0_20200401000001](https://isd.digital.nhs.uk/trud/users/guest/filters/0/categories/9/items/9/releases)
@@ -76,6 +81,7 @@ MELD-B refers to various diagnostic code formats included in target datasets.
 Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are defined in JSON format within `PHEN_assign_v3.json`. 
 
 #### Defining the Strucutre for Folders and Files:
+
 ```
 "folder":"codes/Medication code source",
 "description":"Medication Codes - downloaded 15/12/23",
@@ -87,6 +93,7 @@ Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are de
 ```
 
 #### Define Column Code Types
+
 ```
 "columns":{
 	"read2_code":"READCODE",
@@ -95,11 +102,13 @@ Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are de
 ```
 
 #### Define Concepts to be mapped to
+
 ```
 "meldb_phenotypes": ["ALL_MEDICATIONS"]
 ```
 
 #### Actions: Additional preprocessing (if required):
+
 - In certain cases where you wish to sub-divde a code list table or a column features multiple code types additional processing is required. Add a `action` object inside of the `file` object.
 
 - Table with a sub-categorical column:
@@ -127,15 +136,16 @@ Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are de
 
 *<b>Large Code lists</b> with numerous phenotypes (e.g. Ho et al), require lots of JSON to be generated. See the "Ho generate JSON" section in process_codes_WP.ipynb for example code to generate 
 
+## Usage
 
-
-## ⚡ Usage
 Script preprocess code lists and to map to given concept/phenotype
 
 ### Execution (Bash Script)
+
 `bash ./run.sh`
 
 ### Execution (Shell Command)
+
 usage: `python main.py [-h] [-r2] [-r3] [-i] [-s] [-o] [-a] [-m] [-c] [--no-translate] [--no-verify] [--output] [--error-log] mapping_file`
 
 positional arguments:
@@ -157,9 +167,10 @@ optional arguments:
 
 > **_EXAMPLE:_**  `python main.py PHEN_assign_v3.json -r2 --output output/MELD_concepts_readv2.csv --error-log output/MELD_errors.csv`
 
-## ❤️ Contributing
+## Contributing
 
 ### Commit to GitLab
+
 ```
 git add .
 git commit -m "my message ..."
@@ -167,12 +178,14 @@ git tag -a v1.0.0 -m "added features ..."
 git push
 ```
 
-## 🏦 Funding 
+## Funding 
+
 This project has received funding from the National Institute of Health Research under grant agreement NIHR203988.
 
 <img src="img/nihr-logo-1200-375.jpg" height="100" />
 
-## ⚖️ License
+## License
+
 ![apache2](https://img.shields.io/github/license/saltstack/salt)
 
 This work is licensed under a [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
\ No newline at end of file
-- 
GitLab